Motif IL_44540.5 Version IL_44540.5 of this group appears in releases 1.14 to 1.14
#S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | 3 | break | 4 | 5 | 1-2 | 1-5 | 2-5 | 3-4 | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | IL_1FJG_051 | 1FJG | 0.6164 | 0 | Not an internal loop (H) | A | SSU rRNA | G | 1274 | A | 1275 | G | 1276 | * | C | 1259 | C | 1260 | ntHS | cWW | ||
2 | IL_4NVV_073 | 4NVV | 0.5079 | 1 | A | 23S Ribosomal RNA | G | 1877 | A | 1879 | G | 1880 | * | C | 1915 | C | 1916 | cWW | ncWS | cWW | ||
3 | IL_3U5F_071 | 3U5F | 0.4283 | 0 | 6 | 18S rRNA | C | 1306 | U | 1307 | G | 1308 | * | C | 1317 | G | 1318 | cSH | cWW | tHS | cWW | |
4 | IL_4BPP_069 | 4BPP | 0.3044 | 0 | A | 18S RRNA | C | 1278 | U | 1279 | G | 1280 | * | C | 1289 | G | 1290 | cSH | cWW | tHS | cWW | |
5 | IL_4A1B_020 | 4A1B | 0.3724 | 0 | 1 | 26S RRNA | C | 470 | A | 471 | C | 472 | * | G | 506 | G | 507 | ncWW | ntHS | cWW | ||
6 | IL_4BPP_005 | 4BPP | 0.5332 | 0 | A | 18S RRNA | C | 49 | A | 50 | U | 51 | * | A | 420 | G | 421 | cWW | tHS | cWW | ||
7 | IL_2AW7_004 | 2AW7 | 0.5992 | 0 | A | 16S ribosomal RNA | C | 54 | A | 55 | U | 56 | * | A | 356 | G | 357 | cWW | tHS | cWW | ||
8 | IL_1FJG_004 | 1FJG | 0.5862 | 0 | Minor groove platform (H) | A | SSU rRNA | C | 54 | A | 55 | U | 56 | * | A | 356 | G | 357 | cWW | tHS | cWW | |
9 | IL_3U5F_005 | 3U5F | 0.5405 | 0 | 6 | 18S rRNA | C | 50 | A | 51 | U | 52 | * | A | 428 | G | 429 | cWW | tHS | cWW | ||
10 | IL_1FJG_052 | 1FJG | 0.6077 | 0 | A | SSU rRNA | C | 1260 | A | 1261 | C | 1262 | * | G | 1273 | G | 1274 | tHS | cWW | |||
11 | IL_2AW7_050 | 2AW7 | 0.6403 | 2 | A | 16S ribosomal RNA | U | 1199 | U | 1202 | C | 1203 | * | G | 1057 | G | 1058 | cWW | tHS | cWW | ||
12 | IL_1FJG_042 | 1FJG | 0.6760 | 2 | Minor groove platform (H) | A | SSU rRNA | U | 1199 | G | 1202 | C | 1203 | * | G | 1057 | G | 1058 | cWW | tHS | cWW | |
13 | IL_3U5F_062 | 3U5F | 0.5842 | 0 | 6 | 18S rRNA | C | 1459 | A | 1460 | C | 1461 | * | G | 1178 | G | 1179 | cWW | cWW | |||
14 | IL_2AW7_067 | 2AW7 | 0.4645 | 0 | A | 16S ribosomal RNA | U | 1440 | A | 1441 | G | 1442 | * | C | 1460 | G | 1461 | cWW | tHS | cWW | ||
15 | IL_2QWY_003 | 2QWY | 0.4019 | 0 | A | SAM-II riboswitch | U | 40 | A | 41 | G | 42 | * | C | 23 | A | 24 | cWW | tHS | cWW | ||
16 | IL_4BPP_059 | 4BPP | 0.3238 | 0 | A | 18S RRNA | C | 1430 | A | 1431 | C | 1432 | * | G | 1150 | G | 1151 | cWW | ntHS | cWW | ||
17 | IL_1FJG_038 | 1FJG | 0.2522 | 0 | Minor groove platform (H) | A | SSU rRNA | C | 1226 | A | 1227 | C | 1228 | * | G | 953 | G | 954 | cWW | ntHS | cWW | |
18 | IL_2AW7_045 | 2AW7 | 0.3158 | 0 | A | 16S ribosomal RNA | C | 1226 | A | 1227 | C | 1228 | * | G | 953 | G | 954 | cWW | ntHS | cWW | ||
19 | IL_2QBG_081 | 2QBG | 0.2327 | 1 | B | 23S rRNA | U | 2438 | C | 2440 | U | 2441 | * | A | 2070 | A | 2071 | cSH | cWW | cWW | ||
20 | IL_4IOA_076 | 4IOA | 0.2415 | 1 | Minor groove platform | X | LSU rRNA | U | 2417 | C | 2419 | C | 2420 | * | G | 2053 | A | 2054 | cSH | cWW | cWW | |
21 | IL_3U5H_099 | 3U5H | 0.2556 | 1 | 5 | 25S rRNA | U | 2807 | C | 2809 | C | 2810 | * | G | 2412 | A | 2413 | cSH | cWW | cWW | ||
22 | IL_4A1B_096 | 4A1B | 0.2450 | 1 | 1 | 26S RRNA | U | 2795 | C | 2797 | C | 2798 | * | G | 2407 | A | 2408 | cSH | cWW | cWW | ||
23 | IL_1S72_075 | 1S72 | 0.2268 | 1 | Minor groove platform (H) | 0 | LSU rRNA | U | 2473 | C | 2475 | C | 2476 | * | G | 2111 | A | 2112 | cSH | cWW | cWW | |
24 | IL_4NVV_081 | 4NVV | 0.2184 | 1 | A | 23S Ribosomal RNA | U | 2450 | C | 2452 | C | 2453 | * | G | 2092 | A | 2093 | cSH | cWW | cWW | ||
25 | IL_4IOA_027 | 4IOA | 0.1381 | 0 | Minor groove platform | X | LSU rRNA | U | 925 | C | 926 | C | 927 | * | G | 875 | A | 876 | cSH | cWW | cWW | |
26 | IL_1S72_035 | 1S72 | 0.0000 | 0 | Minor groove platform (H) | 0 | LSU rRNA | U | 1009 | C | 1010 | C | 1011 | * | G | 956 | A | 957 | cSH | cWW | cWW | |
27 | IL_4NVV_030 | 4NVV | 0.0897 | 0 | A | 23S Ribosomal RNA | U | 959 | C | 960 | C | 961 | * | G | 909 | A | 910 | cSH | cWW | cWW | ||
28 | IL_3U5H_041 | 3U5H | 0.2423 | 0 | 5 | 25S rRNA | U | 1050 | U | 1051 | U | 1052 | * | A | 997 | A | 998 | cWW | tHS | cWW | ||
29 | IL_3U5F_029 | 3U5F | 0.2357 | 0 | 6 | 18S rRNA | A | 518 | C | 519 | A | 520 | * | U | 532 | U | 533 | cWW | ntHS | cWW | ||
30 | IL_1Y0Q_003 | 1Y0Q | 0.2223 | 0 | Minor groove platform | A | Group I catalytic intron | A | 120 | C | 121 | G | 122 | * | C | 192 | U | 193 | cWW | ntHS | cWW | |
31 | IL_1U6B_007 | 1U6B | 0.2699 | 0 | Minor groove platform | B | 197-MER | G | 128 | A | 129 | G | 130 | * | C | 177 | C | 178 | cSH | cWW | tHS | cWW |
32 | IL_2AW7_035 | 2AW7 | 0.4232 | 0 | A | 16S ribosomal RNA | A | 746 | A | 747 | G | 748 | * | C | 658 | U | 659 | cWW | cWW | |||
33 | IL_1VW3_065 | 1VW3 | 0.3467 | 1 | A | 21S ribosomal RNA | U | 2704 | C | 2706 | G | 2707 | * | C | 1970 | A | 1971 | cSH | cWW | cWW | ||
34 | IL_2QWY_006 | 2QWY | 0.3922 | 0 | B | SAM-II riboswitch | U | 40 | A | 41 | G | 42 | * | C | 23 | A | 24 | cWW | cWW | |||
35 | IL_2GDI_007 | 2GDI | 0.4082 | 0 | Y | TPP riboswitch | C | 23 | C | 24 | U | 25 | * | A | 35 | G | 36 | ncSH | cWW | cWW | ||
36 | IL_2GDI_003 | 2GDI | 0.3701 | 0 | Minor groove platform | X | TPP riboswitch | C | 23 | C | 24 | U | 25 | * | A | 35 | G | 36 | ncSH | cWW | cWW | |
37 | IL_3IWN_001 | 3IWN | 0.4894 | 0 | Minor groove platform | A | C-di-GMP riboswitch | G | 89 | A | 90 | U | 91 | * | A | 2 | C | 3 | ncWW | cWW | ||
38 | IL_1S72_033 | 1S72 | 0.5849 | 0 | Single bulged A (H) | 0 | LSU rRNA | U | 942 | A | 943 | G | 944 | * | C | 1023 | G | 1024 | ncSH | cWW | cWW | |
39 | IL_3RW6_001 | 3RW6 | 0.5092 | 1 | Minor groove platform | H | constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA | U | 53 | A | 55 | U | 56 | * | A | 7 | A | 8 | ncSH | cWW | cWW | |
40 | IL_4IOA_003 | 4IOA | 0.3419 | 0 | Minor groove platform | X | LSU rRNA | U | 447 | C | 448 | C | 449 | * | G | 42 | A | 43 | cSH | cWW | cWW | |
41 | IL_4NVV_003 | 4NVV | 0.3110 | 0 | A | 23S Ribosomal RNA | U | 461 | C | 462 | C | 463 | * | G | 42 | A | 43 | cSH | cWW | cWW | ||
42 | IL_2QBG_008 | 2QBG | 0.1837 | 0 | B | 23S rRNA | U | 434 | C | 435 | C | 436 | * | G | 43 | A | 44 | cSH | cWW | cWW | ||
43 | IL_4A1B_128 | 4A1B | 0.3709 | 0 | 1 | 26S RRNA | U | 3338 | C | 3339 | U | 3340 | * | A | 3281 | A | 3282 | cWW | cWW | |||
44 | IL_1X8W_004 | 1X8W | 0.5022 | 0 | A | Tetrahymena ribozyme RNA | G | 129 | U | 130 | U | 131 | * | A | 192 | C | 193 | ncSH | cWW | cWW | ||
45 | IL_4A1B_049 | 4A1B | 0.4771 | 1 | 1 | 26S RRNA | G | 1039 | C | 1041 | U | 1042 | * | A | 1062 | C | 1063 | cWW | cWW |
3D structures
Complete motif including flanking bases
Sequence | Counts |
---|---|
CAC*GG | 6 |
CAU*AG | 4 |
UACC*GA | 4 |
UCC*GA | 4 |
GAG*CC | 2 |
CUG*CG | 2 |
UAG*CG | 2 |
UAG*CA | 2 |
GA*UCC | 2 |
CCU*AG | 2 |
GAAG*CC | 1 |
UCAUC*GG | 1 |
UCAGC*GG | 1 |
UACU*AA | 1 |
GA*UACC | 1 |
UUU*AA | 1 |
ACA*UU | 1 |
ACG*CU | 1 |
AAG*CU | 1 |
UACG*CA | 1 |
GAU*AC | 1 |
UAAU*AA | 1 |
UCU*AA | 1 |
GUU*AC | 1 |
GACU*AC | 1 |
Non-Watson-Crick part of the motif
Sequence | Counts |
---|---|
A* | 18 |
C* | 9 |
AC* | 7 |
U* | 4 |
AA* | 2 |
*C | 2 |
CAU* | 1 |
CAG* | 1 |
*AC | 1 |
Release history
Release | 1.14 |
---|---|
Date | 2014-04-27 |
Status | Updated, 1 parent |
Parent motifs
Parent motif | Common motif instances | Only in IL_44540.5 | Only in the parent motif |
---|---|---|---|
IL_44540.4 Compare | IL_1FJG_038, IL_4BPP_069, IL_2AW7_050, IL_1FJG_004, IL_4IOA_076, IL_2QBG_008, IL_2AW7_004, IL_2QWY_006, IL_1FJG_042, IL_2GDI_007, IL_2QWY_003, IL_2AW7_035, IL_2GDI_003, IL_3U5F_029, IL_3U5F_062, IL_1Y0Q_003, IL_2QBG_081, IL_4BPP_059, IL_3IWN_001, IL_1U6B_007, IL_1X8W_004, IL_2AW7_045, IL_3U5H_041, IL_4A1B_020, IL_2AW7_067, IL_4A1B_049, IL_4A1B_128, IL_1FJG_052, IL_1FJG_051, IL_1S72_075, IL_4IOA_027, IL_3RW6_001, IL_4IOA_003, IL_1S72_033, IL_3U5F_071, IL_1S72_035, IL_3U5F_005, IL_4A1B_096, IL_4BPP_005, IL_3U5H_099 | IL_1VW3_065, IL_4NVV_003, IL_4NVV_081, IL_4NVV_073, IL_4NVV_030 | IL_3V2F_070, IL_3V2F_028, IL_3V2F_078 |
Children motifs
Child motif | Common motif instances | Only in IL_44540.5 | Only in the child motif |
---|---|---|---|
IL_44540.6 Compare | IL_2QBG_081, IL_4BPP_069, IL_2AW7_050, IL_1FJG_004, IL_4IOA_076, IL_2QBG_008, IL_2AW7_004, IL_2QWY_006, IL_1FJG_042, IL_2GDI_007, IL_2QWY_003, IL_2AW7_035, IL_2GDI_003, IL_1VW3_065, IL_3U5F_029, IL_3U5F_062, IL_1Y0Q_003, IL_4NVV_003, IL_4BPP_005, IL_4BPP_059, IL_3IWN_001, IL_1FJG_038, IL_4NVV_081, IL_2AW7_045, IL_1X8W_004, IL_3U5H_041, IL_4A1B_020, IL_2AW7_067, IL_4A1B_049, IL_4A1B_128, IL_1FJG_052, IL_1FJG_051, IL_1S72_075, IL_4IOA_027, IL_3RW6_001, IL_4IOA_003, IL_1S72_033, IL_1U6B_007, IL_3U5F_071, IL_1S72_035, IL_4NVV_073, IL_3U5F_005, IL_4NVV_030, IL_4A1B_096, IL_3U5H_099 | IL_4CUX_068, IL_4CUV_102, IL_4CUV_044, IL_4CUX_028, IL_4CUX_029, IL_4CUX_058 |
- Annotations
-
- (30)
- Minor groove platform (8)
- Minor groove platform (H) (5)
- Not an internal loop (H) (1)
- Single bulged A (H) (1)
- Basepair signature
- cWW-cSH-tHS-cWW
- Heat map statistics
- Min 0.06 | Avg 0.50 | Max 1.00
Coloring options: